Every team is going to have some injuries in their organization. In 2013, it seemed like a particularly bad year for the Rays. Three top 10 prospects went down with season ending injuries, and by my count, eight in our writers' top 30 pre-season poll missed time with an injury this year. They range from pretty insignificant to a few that could have significant effects on their careers.
No big deal
OF Brandon Guyer (finger): At first, Guyer was expected to be out for the season when he broke a finger, but it turned out to be no big deal when he came back a month later for the end of Durham's season. It probably is a big deal to him though because he was placed on the 60 day DL anyway to accommodate some of the team's late season additions. He posted a .892 OPS in 32 plate appearances once he came back, and I'd imagine he'd like to be playing in the majors.
RHP Alex Colome (elbow): Days after being optioned to Durham in July, Colome was almost quietly placed on the disabled list with an elbow strain and never returned. I would think that there would be more news on a really good pitching prospect missing two months with an elbow injury, but if there is, it eluded me. It was great to see him make his big league debut, but he only has 178 innings pitched over the last two years combined.
RHP Jesse Hahn (arm): I couldn't find anything more specific than "arm" for Hahn, but it's not really shocking after he missed about two seasons because of Tommy John surgery. Between the cautious approach the Rays had with him this year and the month he missed on the DL late in the season, he only threw 17 more innings than last season. His 79 innings were really effective, but it's fair to question if he has the durability to start.
RHP Parker Markel (shoulder): After experiencing shoulder pain in early July, Markel made one more start and was shut down for the season. I suspect it may have been bothering him longer than that, because he wasn't very good from day one with Charlotte. Going into the year, he appeared at #21 on the writers poll, and after posting a 6.37 ERA and 1.63 WHIP this year, I don't expect to see him on there again going into 2014. It would be great to explain away his entire season because of a shoulder issue, but I don't know if that can be done in good faith.
LHP Mike Montgomery (forearm): Montgomery's delivery has always raised questions about the potential for arm trouble, but he's always survived with only minor issues. He dodged a major bullet again in April this year when he missed just a month with forearm soreness. Whether it was because of the elbow or not, he was mostly ineffective again this season. His walk rate remained above 10%, and his strikeout rate continued to decline. He was better against lefties though, allowing a .656 OPS against them compared to .798 against righties.
RHP Taylor Guerrieri (elbow): Tommy John surgery is never good, but Guerrieri is still young. He can still come back and be effective, but it's a shame that he'll likely miss the entire 2014 season after being shut down in July. He'll be 22 in 2015 and ready to resume his career. Despite concerns about his velocity popping up every so often in his brief pro career so far, he had pitched very well, and his stock was on the rise. It's tougher to see him in top 50 lists now, but the potential should still be there after rehab.
SS Hak-Ju Lee (knee): In April after Lee went down with torn knee ligaments, I wrote a bit about the history of baseball players suffering similar injuries. The good news is the time for rest and rehab is pretty similar for most players, and he should be ready to start 2014 in Durham again. He got off to a great start, and he'll still only be 23 next season. With Yunel Escobar's very reasonable $5 million team option for next season, there is no reason to rush Lee back. While a couple players coming back from similar injuries would suffer similar injuries again, I don't think that's enough evidence to say Lee is now more prone to knee problems than any other shortstop.
CF Ty Morrison (elbow): Morrison had a very nice 2012 season between Charlotte and Montgomery to get back onto top 30 lists. He only got 80 plate appearances in 2013 though, and he had to undergo Tommy John surgery himself. It was a key year for him to show the improvements he made in his plate approach were sustainable in the upper levels. His arm was never a strong point in his game, but I don't know if there's a history of position players' arm strength declining after getting the surgery. One piece of anecdotal evidence comes from Kelly Johnson; after he had the surgery in 2006, he moved from the outfield to second base, but there could have been other factors involved in that decision.